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| Status |
Public on Mar 02, 2016 |
| Title |
3B4-R |
| Sample type |
SRA |
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| Source name |
lymphoid tissue
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| Organism |
Mus musculus |
| Characteristics |
cell type: Resting B cells from the spleen
passages: Sorted (CD43 negative) primary cells
strain: mixed background 129/C58BL/6
genotype: homozygous hs3b-hs4 KO animals, ref Pinaud et al. Immunity. 2001 Aug;15(2):187-99. PubMed PMID: 11520455.s
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy kit (Qiagen) from either freshly purified splenic B cells, obtained after gradient separation using Lympholyte Mammal (Cedarlane) followed by CD43 negative selection (Miltenyi Biotec), or from purified splenic B cells stimulated in vitro (106 cells m/L) for 48 hours in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 5µg/mL LPS (Cayla Invivogen), separated on a Lympholyte Mammal gradient. For each genotype (wt, 3’PALD/D, hs3b-4D/D, 3’RRD/D), RNA sample was prepared from a pool of equivalent numbers of purified B cells from 4 animals
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations. Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
STAR_2.4.0a paired-end mapping versus mm10.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Kallisto v0.42.3 transcripts quantification with Ensembl release 79 GTF file.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts_table.txt: raw counts from featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file. Kallisto_estcounts_table.txt: estimate counts produce with kallisto v0.42.3 with Ensembl release 79 GTF file. Kallisto_tpm_table.txt: transcript counts per million produce with kallisto v0.42.3 with Ensembl release 79 GTF file. BigWig files has been generated using samtools to discriminate expression strand for paired-end reads then genomeCoverageBed and bedGraphToBigWig from bedtools 2 suite.
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| Submission date |
Dec 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE76217 |
RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models |
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| Relations |
| BioSample |
SAMN04359437 |
| SRA |
SRX1494396 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1976948_3B4-R.neg.bw |
110.5 Mb |
(ftp)(http) |
BW |
| GSM1976948_3B4-R.pos.bw |
113.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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